I posted this in another forum but so figured I'd just re-paste it here:
Most manufacturers have a bunkhouse DP now and it's probably not a stretch to custom fit bunkbeds in a model that doesn't have bunks if the rest of the floorplan works better for you.
Your choice will likely be very influenced by your budget and how much you plan on using it. If you can afford it (and don't mind spending more money), there's probably no real good reason to go with the gassers over DPs. Used models are available but bunkhouses are relatively new and there aren't tons sold to being with so on the used market, they aren't easy to find. For new, in case you weren't aware, you can likely get 25%+ of MSRP (although this varies a lot from manufacturer and from dealer). Couple of things to consider as well are how much storage space do they have and do you think you'll need and towing capacity if you plan on towing anything bigger than a car.
Personally, my favorite based on floorplan (I've never seen on in person) is the Fleetwood Discovery 42A. The advantage of that floorplan is that it's also 1 1/2 bath and has an actual room for the kids as oppose to 'bunks in the hallway' like most class A bunkhouses. Also has the master bdrm separated from the kids bdrm by the bathroom so might be a bit better for noise.
I think Winnebago and Gulfstream also had bunkhouses where there was more of a 2nd room (there are probably others although the vast majority have the same layout as the Allegro with the bunks in opposite the bathroom).
Newmar had a model with a loft above the bedroom but it hasn't been in production for a few years and sales were pretty limited so they are a bit hard (but not impossible) to find. It's the Newmar ATME3950 and ATME3951 and from what I've read, they only built about 30 or 40 from 2007 to 2009 so they are not easy to find. There was also a 2010 Newmar ATME4159 for one year but from what I've read, only 3 were built and there was very limited space in the loft area. I actually really like this floorplan (and would certainly consider it in the future for myself) although I've never seen it in person and I've heard complaints about having very limited storage space. I think they were about $240k new so that gives you an idea what to pay used. If you are interested in the 3950/3951, I think the 08 was bit better than the 07 (more power, possibly added the 'Comfort Drive' system (or something like that)).
Bunkhouses with a bit of an extra room:
Fleetwood Discovery 42A (2011 Discovery 42A Floor Plan & Specs : Fleetwood RV
) (Discovery 40G and Expedition 38B (was Bounder Diesel last year) also have bunks - (http://www.fleetwoodrv.com/brandtomo...pedition&m=38B
Winnebago Journey Express 39N (Winnebago Motor Homes - 2011 Journey Express
) (not really closed off but probably not hard to add folding door or something)
Gulfstream Tourmaster T40U (Tourmaster Luxury Class A Motorhome
) (was sold Crescendo 40UL and as another model for a while)
Newmar AllStar (3950/3951) (http://www.newmarcorp.com/uploads/brochu......../archive/2008/2008%20ATME%20Brochure.pdf
Newmar AllStar 4159 (http://www.newmarcorp.com/uploads/fl...llStar4159.pdf
) (also 4154 has hallway bunks)
Cross Country 385DS (http://www.coachmenrv.com/products/cross........?page=floorplandetailsmh&floorplanid= 237
) (forgot about this one)
Other DP bunkhouses:
ForestRiver Berkshire 390BH (http://www.forestriverinc.com/nd/default........kshire&nav=rec&name=116&series=berk shire
ForestRiver Charleston 430BH (tag axle) (http://www.forestriverinc.com/nd/default........=charles&nav=rec&name=208&series=ch arles
Newmar Ventana 3943 (http://www.newmarcorp.com/uploads/floorp........dfs/ventana/2011_VTDP_3943_coloredin.pdf
Newmar DutchStar 4043T (http://www.newmarcorp.com/uploads/fl..._coloredin.pdf
) (I believe this can be factory ordered with optional bunks (personally if I was looking at this, I'd ask if they can do a 4386 with bunks so that you can close off the area and walk through the bathroom))
Tiffin Phaeton 40 QKH (Tiffin Motorhomes
) (big brother of the Allegro posted above)
Damon Astoria 40BQ (2011 Astoria Floorplans | Astoria by Thor Motor Coach
There are likely others but that's all I can think of off the top of my head.